LAMMPS (12 Jun 2025 - Development - patch_12Jun2025-312-gf3113317cc-modified)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread.
  using 1 OpenMP thread(s) per MPI task
## srp_react example script
## Author: Vaibhav Palkar
##
## Simulates controlled degradation of a nanogel particle
## in a simulation box and prints statistics regarding
## the fraction of bonds broken over time.

variable       rseeddpd  equal  26817
variable       rseedvel  equal  5991
variable       breakstep equal  10
variable       probbreak  equal 0.0009
variable       rseedbreak equal 6777

# simulation time
#***********************************************
variable       mainsteps     equal  10000

# simulation setup
#***********************************************
units          lj
atom_style     molecular
boundary       p  p  p
bond_style     harmonic
#lattice        fcc   3.0
comm_modify    cutoff 4.0 vel yes

# initial nanogel
#***********************************************
read_data   gel_equil.dat
Reading data file ...
  orthogonal box = (0 0 0) to (15 15 15)
  1 by 1 by 1 MPI processor grid
  reading atoms ...
  11017 atoms
  reading velocities ...
  11017 velocities
  scanning bonds ...
  4 = max bonds/atom
  orthogonal box = (0 0 0) to (15 15 15)
  1 by 1 by 1 MPI processor grid
  reading bonds ...
  892 bonds
Finding 1-2 1-3 1-4 neighbors ...
  special bond factors lj:    0        0        0       
  special bond factors coul:  0        0        0       
     4 = max # of 1-2 neighbors
     4 = max # of 1-3 neighbors
     8 = max # of 1-4 neighbors
    12 = max # of special neighbors
  special bonds CPU = 0.001 seconds
  read_data CPU = 0.034 seconds

# define groups, create solvent atoms
#**************************************************
group          Npoly         type   1 2 3 4
858 atoms in group Npoly
group          water         type   5
9267 atoms in group water
group          N_all         type   1 2 3 4 5
10125 atoms in group N_all

# density check
#***********************************************
variable       N_atoms  equal  count(all)
variable       tdens equal count(all)/vol
print          "The system density is now ${tdens}"
The system density is now 3.2642962962963

# bond break settings
# #***********************************************
fix            break  N_all     bond/break  ${breakstep}   2   0  prob   ${probbreak}    ${rseedbreak}
fix            break  N_all     bond/break  10   2   0  prob   ${probbreak}    ${rseedbreak}
fix            break  N_all     bond/break  10   2   0  prob   0.0009    ${rseedbreak}
fix            break  N_all     bond/break  10   2   0  prob   0.0009    6777

# interaction parameter setting
#***********************************************
mass             *   1.0
bond_coeff       *   500.0   0.70
special_bonds  lj   1  1  1
Finding 1-2 1-3 1-4 neighbors ...
  special bond factors lj:    1        1        1       
  special bond factors coul:  0        0        0       
     4 = max # of 1-2 neighbors
     4 = max # of 1-3 neighbors
     8 = max # of 1-4 neighbors
    12 = max # of special neighbors
  special bonds CPU = 0.001 seconds
newton         on

pair_style     hybrid dpd  1.0  1.0  ${rseeddpd} srp/react 0.8 * mid break
pair_style     hybrid dpd  1.0  1.0  26817 srp/react 0.8 * mid break
#***********************************************
pair_coeff     *5     *5   dpd   78.000    4.5   1.0
pair_coeff     *4      5   dpd   79.500    4.5   1.0
pair_coeff     *5      6   none
pair_coeff      6      6   srp/react   80.00 0.800

# initial velocity
#***********************************************
velocity       all create 1.0 ${rseedvel} dist gaussian mom yes
velocity       all create 1.0 5991 dist gaussian mom yes

# integrator control
#***********************************************
neighbor       0.3 bin
neigh_modify   every 1 delay 5 check  no
timestep       0.02

# Access variables of fix bond/break
#**********************************************
variable      Nbreak    equal  f_break[2]   # Number of bonds broken
variable      TIME      equal  time

# ensemble setting
#***********************************************
fix            1  all  nve

# print bonds breaking stats
# ***********************************************
variable TotBreak equal 100 # total breakable bonds in current system
#fix print_bonds_broken all print 100 "${TIME} ${Nbreak} $((v_TotBreak-v_Nbreak)/v_TotBreak)" file bonds_broken.txt screen no title "time bonds_broken fraction_bonds_intact"

# thermo output
#***********************************************
thermo         100
thermo_style   custom step temp pe ke etotal epair
thermo_modify  norm  no

reset_timestep 0
#dump          1 Npoly   custom 5000 traj.lammpstrj id type x y z
#*********************************************
run           ${mainsteps}
run           10000

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Your simulation uses code contributions which should be cited:

- pair srp command: doi:10.1063/1.3698476

@Article{Sirk2012
 author = {T. W. Sirk and Y. R. Sliozberg and J. K. Brennan and M. Lisal and J. W. Andzelm},
 title = {An Enhanced Entangled Polymer Model for Dissipative Particle Dynamics},
 journal = {J.~Chem.\ Phys.},
 year =    2012,
 volume =  136,
 pages =   {134903}
}

- pair srp/react style: doi:10.1021/acs.jpcb.1c09570

@Article{palkar2022
 author = {Palkar, Vaibhav and Kuksenok, Olga},
 title = {Controlling Degradation and Erosion of Polymer Networks: Insights from Mesoscale Modeling},
 journal = {J.~Phys.\ Chem.~B},
 year = 2022,
 volume = 126,
 number = 1,
 pages = {336--346}
}

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Using type 6 for bond particles
Thermo normalization turned off by pair srp/react
Generated 0 of 15 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
  update: every = 1 steps, delay = 5 steps, check = no
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 1.3
  ghost atom cutoff = 4
  binsize = 0.65, bins = 24 24 24
  3 neighbor lists, perpetual/occasional/extra = 3 0 0
  (1) pair dpd, perpetual, skip from (3)
      attributes: half, newton on
      pair build: skip
      stencil: none
      bin: none
  (2) pair srp/react, perpetual, skip from (3)
      attributes: half, newton on
      pair build: skip
      stencil: none
      bin: none
  (3) neighbor class addition, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d
      bin: standard
Removed/inserted 892/892 bond particles.
Per MPI rank memory allocation (min/avg/max) = 24.35 | 24.35 | 24.35 Mbytes
   Step          Temp          PotEng         KinEng         TotEng         E_pair    
         0   1.0009302      127698.37      15200.126      142898.49      127171.17    
       100   1.0051051      127732.67      15263.527      142996.2       127169.51    
Removed/inserted 892/891 bond particles.
       200   1.0031001      127653.37      15233.078      142886.45      127071.53    
Removed/inserted 891/890 bond particles.
       300   1.0246589      127758.8       15560.469      143319.27      127196.75    
       400   1.0093479      127841.96      15327.957      143169.91      127237.13    
Removed/inserted 890/889 bond particles.
       500   1.0056122      127569.07      15271.228      142840.29      126985.24    
       600   1.0130736      127660.55      15384.535      143045.09      127071.24    
Removed/inserted 889/888 bond particles.
Removed/inserted 888/887 bond particles.
       700   1.0129349      127641.6       15382.429      143024.02      127088.88    
Removed/inserted 887/886 bond particles.
       800   1.0098758      127750.89      15335.974      143086.87      127187.31    
Removed/inserted 886/885 bond particles.
       900   1.0148196      127670.63      15411.051      143081.68      127132.51    
Removed/inserted 885/884 bond particles.
Removed/inserted 884/883 bond particles.
      1000   1.008631       127584.46      15317.07       142901.53      127035.71    
Removed/inserted 883/882 bond particles.
      1100   1.006977       127802.95      15291.953      143094.91      127268.62    
Removed/inserted 882/881 bond particles.
Removed/inserted 881/880 bond particles.
      1200   1.014135       127713.87      15400.654      143114.53      127158.41    
      1300   1.0070067      127720.36      15292.403      143012.76      127142.94    
Removed/inserted 880/879 bond particles.
      1400   1.0131222      127676.46      15385.274      143061.73      127106.96    
Removed/inserted 879/878 bond particles.
      1500   1.0097574      127734.62      15334.176      143068.8       127186.48    
Removed/inserted 878/877 bond particles.
      1600   1.0227217      127586.53      15531.052      143117.58      127046.79    
      1700   1.0134232      127599.01      15389.845      142988.85      127036.35    
      1800   1.01583        127773.32      15426.394      143199.71      127209.88    
Removed/inserted 877/876 bond particles.
      1900   0.99827708     127753.44      15159.836      142913.27      127215.56    
Removed/inserted 876/875 bond particles.
      2000   0.9978551      127639.36      15153.428      142792.79      127099.78    
Removed/inserted 875/874 bond particles.
      2100   1.0130762      127546.21      15384.575      142930.78      126982.79    
Removed/inserted 874/873 bond particles.
      2200   1.0143324      127592.75      15403.652      142996.4       127027.14    
      2300   1.0164156      127620.54      15435.288      143055.83      127086.03    
Removed/inserted 873/871 bond particles.
      2400   1.0160835      127662.43      15430.243      143092.68      127138.71    
      2500   1.0110011      127676.29      15353.063      143029.36      127133.98    
Removed/inserted 871/870 bond particles.
      2600   1.025616       127596.3       15575.004      143171.31      127056.47    
      2700   1.0140385      127579.4       15399.188      142978.58      127031.2     
      2800   1.0107345      127674.32      15349.014      143023.33      127154.3     
Removed/inserted 870/869 bond particles.
      2900   1.014851       127697.88      15411.527      143109.41      127124.97    
      3000   1.023451       127479.67      15542.127      143021.8       126944.31    
      3100   1.0063862      127617.86      15282.981      142900.84      127059.86    
Removed/inserted 869/868 bond particles.
      3200   1.0085388      127684.8       15315.67       143000.47      127117.94    
Removed/inserted 868/867 bond particles.
      3300   1.0106531      127619.65      15347.777      142967.43      127092.66    
Removed/inserted 867/866 bond particles.
      3400   1.0285951      127656.02      15620.245      143276.27      127110.61    
      3500   1.0044666      127734.81      15253.83       142988.64      127198.64    
Removed/inserted 866/864 bond particles.
      3600   1.0199668      127663.62      15489.216      143152.83      127116.52    
Removed/inserted 864/863 bond particles.
Removed/inserted 863/862 bond particles.
      3700   1.0150843      127866.2       15415.071      143281.27      127304.89    
Removed/inserted 862/861 bond particles.
      3800   1.0235787      127827.32      15544.066      143371.39      127269.97    
      3900   1.0198965      127837.41      15488.149      143325.56      127261.73    
      4000   1.0050188      127664.05      15262.215      142926.27      127130.78    
Removed/inserted 861/860 bond particles.
      4100   1.0139624      127710.18      15398.033      143108.22      127157.81    
      4200   1.012348       127593.66      15373.517      142967.17      127075.56    
      4300   1.0151444      127639.37      15415.982      143055.35      127136.1     
Removed/inserted 860/859 bond particles.
Removed/inserted 859/858 bond particles.
      4400   1.0321693      127529.83      15674.524      143204.35      127010.67    
Removed/inserted 858/857 bond particles.
Removed/inserted 857/855 bond particles.
      4500   1.0182479      127775.9       15463.113      143239.02      127239.81    
Removed/inserted 855/854 bond particles.
      4600   1.0106075      127848.36      15347.086      143195.44      127312.01    
Removed/inserted 854/853 bond particles.
      4700   1.02785        127851.54      15608.931      143460.47      127345.86    
      4800   1.0019535      127647.04      15215.665      142862.71      127108.4     
Removed/inserted 853/851 bond particles.
      4900   0.99889241     127721.22      15169.18       142890.4       127202.83    
      5000   0.99526757     127617.64      15114.133      142731.78      127107.64    
Removed/inserted 851/850 bond particles.
      5100   1.0158888      127660.65      15427.288      143087.94      127107.57    
      5200   1.0186127      127704.43      15468.652      143173.08      127175.53    
      5300   1.0196894      127738.3       15485.003      143223.3       127188.62    
      5400   1.0147346      127757.76      15409.759      143167.52      127281.66    
Removed/inserted 850/849 bond particles.
Removed/inserted 849/848 bond particles.
      5500   1.0124364      127711.94      15374.86       143086.8       127210.66    
      5600   1.0136572      127809.38      15393.399      143202.78      127260.76    
      5700   1.0136689      127582.37      15393.576      142975.94      127030.63    
Removed/inserted 848/847 bond particles.
      5800   1.0182465      127532.02      15463.091      142995.11      126972.43    
      5900   1.013586       127490.18      15392.316      142882.5       126951.28    
Removed/inserted 847/846 bond particles.
      6000   1.0142507      127493.76      15402.411      142896.17      126968.81    
      6100   1.0075303      127375.06      15300.355      142675.42      126848.6     
      6200   1.0020015      127440.66      15216.395      142657.06      126940.68    
Removed/inserted 846/845 bond particles.
      6300   1.016057       127420.83      15429.842      142850.67      126930.79    
Removed/inserted 845/844 bond particles.
      6400   1.0149399      127690.64      15412.878      143103.52      127166.25    
Removed/inserted 844/843 bond particles.
      6500   0.99646255     127657.64      15132.28       142789.92      127136.79    
      6600   1.0139147      127577.17      15397.308      142974.48      127072.39    
      6700   1.0092811      127648.61      15326.943      142975.55      127114.14    
      6800   1.0069166      127498.78      15291.035      142789.82      126965.74    
      6900   1.0061292      127783.69      15279.078      143062.77      127280.45    
Removed/inserted 843/842 bond particles.
      7000   1.0104769      127848.37      15345.102      143193.47      127324.7     
      7100   1.0087376      127648.48      15318.689      142967.17      127130.06    
      7200   1.0128129      127698.11      15380.577      143078.69      127175.59    
      7300   1.0086591      127552.01      15317.497      142869.51      127003.07    
      7400   1.0106178      127558.55      15347.242      142905.79      127014.78    
      7500   1.0201698      127665.85      15492.298      143158.15      127162.82    
      7600   1.0131341      127622.9       15385.455      143008.36      127042.27    
      7700   1.0258714      127633.98      15578.883      143212.87      127126.28    
      7800   1.0036517      127518.35      15241.455      142759.81      127038.62    
      7900   0.99637773     127545.03      15130.992      142676.02      127048.4     
      8000   1.0122962      127638.71      15372.73       143011.44      127130.13    
Removed/inserted 842/841 bond particles.
      8100   1.0230725      127607.73      15536.379      143144.11      126996.93    
      8200   1.0155936      127738.8       15422.804      143161.6       127211.15    
      8300   1.016122       127563.94      15430.829      142994.77      127006.78    
      8400   1.0226653      127654.71      15530.196      143184.9       127155.6     
Removed/inserted 841/840 bond particles.
      8500   1.0012219      127732.51      15204.556      142937.07      127193.57    
      8600   1.0109858      127693.79      15352.83       143046.62      127176.37    
Removed/inserted 840/839 bond particles.
      8700   1.0042339      127537.2       15250.296      142787.49      127034.53    
      8800   1.0103179      127623.14      15342.687      142965.83      127147.69    
Removed/inserted 839/838 bond particles.
      8900   1.005348       127557.21      15267.215      142824.42      126991.64    
Removed/inserted 838/837 bond particles.
      9000   1.0240137      127497.66      15550.673      143048.34      126976.95    
Removed/inserted 837/836 bond particles.
      9100   1.009437       127673.8       15329.31       143003.1       127199.36    
Removed/inserted 836/835 bond particles.
      9200   1.0164276      127679.84      15435.47       143115.31      127172.92    
      9300   1.0089299      127804.83      15321.61       143126.44      127274.48    
Removed/inserted 835/834 bond particles.
      9400   1.0173733      127753.61      15449.831      143203.44      127190.56    
      9500   1.0129999      127573.39      15383.416      142956.81      127080.08    
      9600   1.0065481      127555.69      15285.44       142841.13      127029.7     
      9700   1.0115131      127711.6       15360.838      143072.44      127211.16    
      9800   1.0141569      127631.89      15400.987      143032.88      127106.32    
Removed/inserted 834/833 bond particles.
      9900   1.006907       127674.02      15290.89       142964.91      127178.33    
Removed/inserted 833/832 bond particles.
     10000   1.0181282      127673.6       15461.295      143134.89      127135.96    
Deleted 832 atoms, new total = 10125
Loop time of 46.6942 on 1 procs for 10000 steps with 10125 atoms

Performance: 370067.259 tau/day, 214.159 timesteps/s, 2.168 Matom-step/s
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 27.706     | 27.706     | 27.706     |   0.0 | 59.33
Bond    | 0.048519   | 0.048519   | 0.048519   |   0.0 |  0.10
Neigh   | 15.161     | 15.161     | 15.161     |   0.0 | 32.47
Comm    | 2.0289     | 2.0289     | 2.0289     |   0.0 |  4.35
Output  | 0.0045366  | 0.0045366  | 0.0045366  |   0.0 |  0.01
Modify  | 1.5693     | 1.5693     | 1.5693     |   0.0 |  3.36
Other   |            | 0.1763     |            |       |  0.38

Nlocal:          10125 ave       10125 max       10125 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:          26497 ave       26497 max       26497 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:              0 ave           0 max           0 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 0
Ave neighs/atom = 0
Ave special neighs/atom = 0.59496296
Neighbor list builds = 2056
Dangerous builds not checked
#***********************************************
Total wall time: 0:00:46
